void renderMolecule(int structure, const char* folder, const char* file, int number, const char* title) {
// render the molecule to file
indigoLayout(structure);
indigoSetOption("render-output-format", "png");
indigoSetOption("render-comment", title);
indigoSetOption("render-comment-position", "top");
indigoSetOptionXY("render-image-size", 400, 500);
indigoSetOptionColor("render-background-color", 1.0, 1.0, 1.0);
char str[256];
if(number != -1) {
sprintf(str, "%s/%d%s%s", folder, number, "_", file);
}
else if(strcmp(folder,"")!=0)
{
sprintf(str, "%s/%s", folder, file);
}
else {
sprintf(str, "%s", file);
}
indigoRenderToFile(structure, str);
}
void renderPair(int s1, int s2, const char* folder, const char* file, int number, const char* title) {
int collection = indigoCreateArray();
indigoArrayAdd(collection, s1);
indigoArrayAdd(collection, s2);
indigoSetOption("render-output-format", "png");
indigoSetOption("render-comment", title);
indigoSetOption("render-comment-position", "top");
indigoSetOptionXY("render-image-size", 800, 1000);
indigoSetOptionColor("render-background-color", 1.0, 1.0, 1.0);
char str[256];
if(number != -1) {
sprintf(str, "./%s/%d%s%s%s", folder, number, "_", file, ".png");
}
else
{
sprintf(str, "%s%s", file, ".png");
}
indigoRenderGridToFile(collection, NULL, 2, str);
indigoFree(collection);
}
int parseParams (Params* p, int argc, char *argv[]) {
int i;
if (strcmp(argv[1], "-") == 0)
{
if (_isReaction(argv[2]))
{
p->mode = MODE_SINGLE_REACTION;
p->string_to_load = argv[2];
}
else
{
p->mode = MODE_SINGLE_MOLECULE;
p->string_to_load = argv[2];
}
if (argc <= 3)
USAGE();
i = 3;
}
else
{
p->infile_ext[0] = 0;
if (strlen(argv[1]) >= 4 && argv[1][strlen(argv[1]) - 4] == '.')
{
p->infile_ext[3] = 0;
strncpy(p->infile_ext, argv[1] + strlen(argv[1]) - 3, 3);
}
else if (strlen(argv[1]) > 7 && argv[1][strlen(argv[1]) - 7] == '.')
{
p->infile_ext[6] = 0;
strncpy(p->infile_ext, argv[1] + strlen(argv[1]) - 6, 6);
}
p->file_to_load = argv[1];
if (strcasecmp(p->infile_ext, "mol") == 0)
p->mode = MODE_SINGLE_MOLECULE;
else if (strcasecmp(p->infile_ext, "rxn") == 0)
p->mode = MODE_SINGLE_REACTION;
else if (strcasecmp(p->infile_ext, "smi") == 0)
{
int reaction;
if (_isMultiline(argv[1], &reaction))
p->mode = MODE_MULTILINE_SMILES;
else
{
if (reaction)
p->mode = MODE_SINGLE_REACTION;
else
p->mode = MODE_SINGLE_MOLECULE;
}
}
else if (strcasecmp(p->infile_ext, "cml") == 0)
{
int reaction;
if (_isMultipleCML(argv[1], &reaction))
p->mode = MODE_MULTIPLE_CML;
else
{
if (reaction)
p->mode = MODE_SINGLE_REACTION;
else
p->mode = MODE_SINGLE_MOLECULE;
}
}
else if (strcasecmp(p->infile_ext, "sdf") == 0 || strcasecmp(p->infile_ext, "sdf.gz") == 0)
p->mode = MODE_SDF;
else if (strcasecmp(p->infile_ext, "rdf") == 0 || strcasecmp(p->infile_ext, "rdf.gz") == 0)
p->mode = MODE_RDF;
else
USAGE();
i = 2;
}
p->outfile = argv[i++];
if (strlen(p->outfile) < 5 || p->outfile[strlen(p->outfile) - 4] != '.')
USAGE();
p->outfile_ext[3] = 0;
strncpy(p->outfile_ext, p->outfile + strlen(p->outfile) - 3, 3);
indigoSetOptionBool("treat-x-as-pseudoatom", 1);
indigoSetOptionBool("render-coloring", 1);
indigoSetOptionBool("render-highlight-color-enabled", 1);
for (; i < argc; i++)
{
if (strcmp(argv[i], "-w") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting number after -w\n");
return -1;
}
if (sscanf(argv[i], "%d", &p->width) != 1 || p->width <= 0)
{
fprintf(stderr, "%s is not a valid width\n", argv[i]);
return -1;
}
}
else if (strcmp(argv[i], "-h") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting number after -h\n");
return -1;
}
if (sscanf(argv[i], "%d", &p->height) != 1 || p->height <= 0)
{
fprintf(stderr, "%s is not a valid height\n", argv[i]);
return -1;
}
}
else if (strcmp(argv[i], "-margins") == 0)
{
int horz, vert;
if (i + 2 >= argc)
{
fprintf(stderr, "expecting two numbers after -margins\n");
return -1;
}
if (sscanf(argv[i + 1], "%d", &horz) != 1 || horz < 0)
{
fprintf(stderr, "%s is not a valid horizontal margin\n", argv[i]);
return -1;
}
if (sscanf(argv[i + 2], "%d", &vert) != 1 || vert < 0)
{
fprintf(stderr, "%s is not a valid vertical margin\n", argv[i + 1]);
return -1;
}
indigoSetOptionXY("render-margins", horz, vert);
i += 2;
}
else if (strcmp(argv[i], "-thickness") == 0)
{
float rt;
if (++i == argc)
{
fprintf(stderr, "expecting number after -thickness\n");
return -1;
}
if (sscanf(argv[i], "%f", &rt) != 1 || rt < 0)
{
fprintf(stderr, "%s is not a valid relative thickness\n", argv[i]);
return -1;
}
indigoSetOptionFloat("render-relative-thickness", rt);
}
else if (strcmp(argv[i], "-linewidth") == 0)
{
float rt;
if (++i == argc)
{
fprintf(stderr, "expecting number after -linewidth\n");
return -1;
}
if (sscanf(argv[i], "%f", &rt) != 1 || rt < 0)
{
fprintf(stderr, "%s is not a valid line width value\n", argv[i]);
return -1;
}
indigoSetOptionFloat("render-bond-line-width", rt);
}
else if (strcmp(argv[i], "-bond") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting number after -bond\n");
return -1;
}
if (sscanf(argv[i], "%d", &p->bond) != 1 || p->bond <= 0)
{
fprintf(stderr, "%s is not a valid bond length\n", argv[i]);
return -1;
}
}
else if (strcmp(argv[i], "-coloring") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting 'on' or 'off' after -coloring\n");
return -1;
}
if (strcasecmp(argv[i], "on") == 0)
indigoSetOptionBool("render-coloring", 1);
else if (strcasecmp(argv[i], "off") == 0)
indigoSetOptionBool("render-coloring", 0);
else
{
fprintf(stderr, "expecting 'on' or 'off' after -coloring\n");
return -1;
}
}
else if (strcmp(argv[i], "-hlthick") == 0)
{
indigoSetOptionBool("render-highlight-thickness-enabled", 1);
}
else if (strcmp(argv[i], "-hlcolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -hlcolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionBool("render-highlight-color-enabled", 1);
indigoSetOptionColor("render-highlight-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-bgcolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -bgcolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionColor("render-background-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-basecolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -basecolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionColor("render-base-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-aamcolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -aamcolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionColor("render-aam-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-dsgcolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -aamcolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionColor("render-data-sgroup-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-hydro") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -hydro\n");
return -1;
}
indigoSetOption("render-implicit-hydrogens-visible", argv[i]);
p->hydro_set = 1;
}
else if (strcmp(argv[i], "-label") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -label\n");
return -1;
}
indigoSetOption("render-label-mode", argv[i]);
}
else if (strcmp(argv[i], "-arom") == 0)
{
p->aromatization = AROM;
}
else if (strcmp(argv[i], "-dearom") == 0)
{
p->aromatization = DEAROM;
}
else if (strcmp(argv[i], "-stereo") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -stereo\n");
return -1;
}
indigoSetOption("render-stereo-style", argv[i]);
}
else if (strcmp(argv[i], "-cdbwsa") == 0)
{
indigoSetOptionBool("render-center-double-bond-when-stereo-adjacent", 1);
}
else if (strcmp(argv[i], "-query") == 0)
{
p->query_set = 1;
}
else if (strcmp(argv[i], "-smarts") == 0)
{
p->smarts_set = 1;
}
else if (strcmp(argv[i], "-id") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -id\n");
return -1;
}
p->id = argv[i];
}
else if (strcmp(argv[i], "-catalysts") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -catalysts\n");
return -1;
}
indigoSetOption("render-catalysts-placement", argv[i]);
}
else if (strcmp(argv[i], "-comment") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -comment\n");
return -1;
}
p->comment = argv[i];
}
else if (strcmp(argv[i], "-commentoffset") == 0)
{
int offset;
if (++i >= argc)
{
fprintf(stderr, "expecting an integer after -commentoffset\n");
return -1;
}
if (sscanf(argv[i], "%d", &offset) != 1 || offset < 0)
{
fprintf(stderr, "%s is not a valid comment offset\n", argv[i]);
return -1;
}
indigoSetOptionInt("render-comment-offset", offset);
}
else if (strcmp(argv[i], "-commentfield") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -commentfield\n");
return -1;
}
p->comment_field = argv[i];
}
else if (strcmp(argv[i], "-commentname") == 0)
{
p->comment_name = 1;
}
else if (strcmp(argv[i], "-commentsize") == 0)
{
int commentsize;
if (++i == argc)
{
fprintf(stderr, "expecting number after -commentsize\n");
return -1;
}
if (sscanf(argv[i], "%d", &commentsize) != 1 || commentsize <= 0)
{
fprintf(stderr, "%s is not a valid font size\n", argv[i]);
return -1;
}
indigoSetOptionFloat("render-comment-font-size", (float)commentsize);
}
else if (strcmp(argv[i], "-commentcolor") == 0)
{
float r, g, b;
if (i + 3 >= argc)
{
fprintf(stderr, "expecting 3 numbers after -commentcolor\n");
return -1;
}
if (parseColor(argv, i, &r, &g, &b) != 0)
return -1;
indigoSetOptionColor("render-comment-color", r, g, b);
i += 3;
}
else if (strcmp(argv[i], "-commentalign") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -commentalign\n");
return -1;
}
indigoSetOption("render-comment-alignment", argv[i]);
}
else if (strcmp(argv[i], "-commentpos") == 0)
{
if (++i == argc)
{
fprintf(stderr, "expecting an identifier after -commentpos\n");
return -1;
}
indigoSetOption("render-comment-position", argv[i]);
}
else if (strcmp(argv[i], "-atomnumbers") == 0)
indigoSetOptionBool("render-atom-ids-visible", 1);
else if (strcmp(argv[i], "-bondnumbers") == 0)
indigoSetOptionBool("render-bond-ids-visible", 1);
else if (strcmp(argv[i], "-onebased") == 0)
indigoSetOptionBool("render-atom-bond-ids-from-one", 1);
else if (strcmp(argv[i], "-help") == 0)
{
usage();
return 0;
}
else
{
fprintf(stderr, "unknown option: %s\n", argv[i]);
return -1;
}
}
if (p->bond > 0)
indigoSetOptionFloat("render-bond-length", (float)p->bond);
if (p->width > 0)
indigoSetOptionInt("render-image-width", p->width);
if (p->height > 0)
indigoSetOptionInt("render-image-height", p->height);
if (p->hydro_set && p->query_set)
{
fprintf(stderr, "-hydro conflicts with -query (implicit hydrogens do not exist in queries)\n");
}
return 0;
}
